The Clock Tower Courtyard is a cloister on the base of the Clock Tower at Hogwarts Castle. This cloister seems to be one of the older parts of the castle and the ceiling and walls are dilapidated. It also leads to the Wooden Bridge and, as it is on a hill, is on the third floor. In the centre of the courtyard is an antique fountain surrounded by statues of eagles. A pear tree also grows in this courtyard.

In the video game adaptation of Harry Potter and the Order of the Phoenix, this is one of the Hogwarts Courtyards in which Harry Potter has to trigger a Portable Swamp. The "Swamped Clock Tower Courtyard" becomes kind of a pool, with slimy, green waters and a lot of vegetation. The fountain which stands in the middle of the courtyard is destroyed in the process. However, in the end of the game, the fountain and courtyard have been restored to their previous state.

The set used to film this courtyard and the interior of the Clock Tower were renovated into the Viaduct Courtyard and Entrance Hall for the film adaptation of Harry Potter and the Goblet of Fire. The set was slightly turned back into the Clock Tower Courtyard for Harry Potter and the Order of the Phoenix.

The fountain in the middle of the courtyard has four statues of an eagle devouring a snake, which is a representation of the Coat of arms of México, a reference to the Prisoner of Azkaban's Director nationality.